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The following are Research Outputs from all resources supported since 2010 that have been reported to Research Computing staff. To list your publications, presentations, grants, awards, students graduated, etc, please contact Alex Pacheco.

Publications

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title2022
  1. K. Zhao, B. Duka, H. Xie, D. J. Oathes, V. Calhoun, and Y. Zhang. "A dynamic graph convolutional neural network framework reveals new insights into connectome dysfunctions in ADHD" NeuroImage, 246: 118774 (2022). doi: 10.1016/j.neuroimage.2021.118774
  2. Z. Liu, C.E. Ekuma, W. Li, J. Yang, X. Li, "ElasTool: An automated toolkit for elastic constants calculation, Computer Physics Communications, 270, 108180 (2022). ISSN 0010-4655, doi: 10.1016/j.cpc.2021.108180


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title2021
  1. G. Repa, L. A. Fredin, "Parameter Space Exploration Reveals Interesting Mn-doped SrTiO3 Structures", Phys. Chem. Chem. Phys, 23, 23486 (2021), doi: 10.1039/D1CP02417E
  2. S. M. Martin, A. N. Oldacre, C. A. Pointer, T. Huang, G. Repa, L. A.  Fredin, and E. R. Young, "Proton-controlled Non-exponential Photoluminescence in a Pyridyl-Amidine-substituted Re(I) complex", Dalton Transactions, 50, 7265 (2021). doi: 10.1039/D1DT01132D
  3. P. Schwarzenberg*, T. Ren*, K. Klein, B. von Rechenberg, S. Darwiche, and H. L. Dailey, "Domain-Independent Simulation of Physiologically Relevant Callus Shape in Mechanoregulated Models of Fracture Healing", Journal of Biomechanics, 118, 110300 (2021). PMID: 33601180 (*equal contribution)
  4. P. Schwarzenberg, K. Klein, S. J. Ferguson, B. von Rechenberg, S. Darwiche, and H. L. Dailey, " Virtual Mechanical Tests Out-Perform Morphometric Measures for Assessment of Mechanical Stability of Fracture Healing In Vivo", Journal of Orthopaedic Research, 39(4), 727 (2021). PMID: 32970350
  5. D. Holz, R. A. Hall, E.  Usukura, S. Yamashiro, N. Watanabe, and D. Vavylonis, "A mechanism with severing near barbed ends and annealing explains structure and dynamics of dendritic actin networks", 2021 (pending revisions for eLife) bioRxiv doi: 10.1101/2021.03.31.437985 
  6. D. M. Rutkowski and D. Vavylonis, "Discrete mechanical model of lamellipodial actin network implements molecular clutch mechanism and generates arcs and microspikes", 2021, PLOS Comp. Biol., accepted, bioRxiv doi: 10.1371/journal.pcbi.1009506 
  7. T. Litschel, C. F. Kelley, D. Holz, M. Adeli Koudehi, S. Kenjiro Vogel, L. Burbaum, N. Mizuno, D. Vavylonis, and  P. Schwille, "Reconstitution of Contractile Actomyosin Rings in Vesicles," Nature Communications 12, 2254 (2021) doi: 10.1038/s41467-021-22422-7
  8. A. Venzie, A. Portoff, C. Fares, M. Stavola, W. B. Fowler, F. Ren, and Stephen J. Pearton,  "OH-Si complex in hydrogenated n-type β-Ga2O3:Si", Appl. Phys. Lett. 119, 062109 (2021).
  9. Y. Fan, X. Tian, X. Yang, X. Li, C. Webster, and Y. Yu, "An asymptotically compatible probabilistic collocation method for randomly heterogeneous nonlocal problems", Submitted (2021).
  10. H. You, Y. Yu, S. Silling, and M. D’Elia, "A data-driven peridynamic continuum model for upscaling molecular dynamics", Preprint (2021).
  11. H. You, Y. Yu, M. DÉlia, T. Gao, and S. Silling, "Nonlocal kernel network (NKN): a stable and resolution-independent deep neural network", Under Review (2021).
  12. M. Foss, P. Radu, Y. Yu, "Convergence analysis and numerical studies for linearly elastic peridynamics with dirichlet-type boundary conditions", arXiv preprint arXiv:2106.13878 (2021).
  13. M. DÉlia, and Y. Yu, "On the prescription of boundary conditions for nonlocal poisson’s and peridynamics models", arXiv preprint arXiv:2107.04450 (2021).
  14. H. You, Y. Yu, N. Trask, M. Gulian, M. D’Elia, Data-driven learning of nonlocal physics from high fidelity synthetic data, Computer Methods in Applied Mechanics and Engineering 374 (2021) 113553.
  15. B. N. Ezealigo, and C. E. Ekuma, "Influence of vacancy defect on the structural and optical properties of hexagonal barium titanate ceramics: Experimental and theoretical analysis", Materials Letters, 304, 130582 (2021) doi: 10.1016/j.matlet.2021.130582
  16. Lalrinkima,  C. E. Ekuma, T. C. Chibueze, L. A. Fomin, I. V. Malikov, L. Zadeng, and D. P. Rai, "Electronic, magnetic, vibrational, and X-ray spectroscopy of inverse full-Heusler Fe2IrSi alloy", Phys. Chem. Chem. Phys., 23, 11876 (2021) doi: 10.1039/D1CP00418B
  17. R.M. Obodo, T. C. Chibueze, I. Ahmad, C. E. Ekuma, A. T. Raji, M. Maaza, and F. I. Ezema, "Effects of copper ion irradiation on CuyZn1−2y−xMny/GOCuyZn1−2y−xMny/GO supercapacitive electrodes". J Appl Electrochem, 51, 829–845 (2021). doi: 10.1007/s10800-021-01543-3
  18. K. J. Fisher, R. C. Vignogna, and G. I. Lang, "Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci", Genome Biol Evol., 13(8), evab181 (2021) doi: 10.1093/gbe/evab181. PMID: 34363476.
  19. R. C. Vignogna, S. W. Buskirk, and G. I. Lang GI. "Exploring a local genetic interaction network using evolutionary replay experiments", Mol Biol Evol., 38(8), 3144–3152(2021). doi: 10.1093/molbev/msab087. PMID: 33749796.
  20. M. Razizadeh, M. Nikfar, and Y. Liu, “Small molecule therapeutics to destabilize the ACE2-RBD complex: A molecular dynamics study,” Biophysical Journal, 120 (14), 2793–2804 (2021), doi: 10.1016/J.BPJ.2021.06.016.
  21. Y. Zhang, W. Wu, R. Toll, S. Naparstek, A. Maron-Katz, M. Watts, J. Gordon, J. Jeong, L. Astolfi, E. Shpigel, P. Longwell, K. Sarhadi, D. EI-Said, Y. Li, C. Cooper, C. Chin-Fatt, M. Arns, M. Goodkind, M. Trivedi, C. Marmar, and A. Etkin, "Identification of psychiatric disorder subtypes from functional connectivity patterns in resting-state electroencephalography", Nature Biomedical Engineering, 5: 309-323 (2021) doi: 10.1038/s41551-020-00614-8
  22. Y. Zhang, H. Zhang, E. Adeli, X. Chen, M. Liu, and D. Shen. "Multiview feature learning with multiatlas based functional connectivity networks for MCI diagnosis", IEEE Transactions on Cybernetics, 2021, Accepted. doi: 10.1109/TCYB.2020.3016953
  23. Y. Zhang, T. Zhou, W. Wu, H. Xie, H. Zhu, G. Zhou, A. Cichocki, "Improving EEG decoding via clustering-based multi-task feature learning". IEEE Transactions on Neural Networks and Learning Systems, 2021, Accepted. doi: 10.1109/TNNLS.2021.3053576

  24. P. M. Wilson, M. L. Chin, C. E. Ekuma, S. Najmaei, K. M. Price, T. Schiros, and J. Hone, "Chlorine-mediated atomic layer deposition of HfO2 on graphene". J. Mater. Chem. C, 9, 17437-17443 (2021). doi:10.1039/D1TC03502A

  25. J. Munshi, A. Roy, S. Hansen, C.E. Ekuma, and G. Balasubramanian, "Effect of vacancy defects on the thermal transport of β-Ga2O3", Molecular Simulation, 47(12), 1017–1021 (2021). doi:10.1080/08927022.2021.1941943


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title2020
  1. Wehrmann, C. M.; Imran, M.; Pointer, C. A.; Fredin, L. A.*; Young, E. R.*; Chen, M. S.*, Spin Multiplicity Effects in Doublet versus Singlet Emission: The Photophysical Consequences of a Single Electron. Chem. Sci., 2020, 11, 10212-10219. (DOI: 10.1039/d0sc04211k)          
  2. Ren T and Dailey HL. Mechanoregulation Modeling of Bone Healing in Realistic Fracture Geometries. Biomechanics and Modeling in Mechanobiology, 19, pp. 2307-2322, 2020. PMID: 32524288
  3. Horan B. G., Hall A., and Vavylonis D., Insights into actin polymerization and nucleation using a coarse grained model, 2020, Biophys. J. 119:553-566. DOI: 10.1016/j.bpj.2020.06.019
  4. “Determination of dielectric axes and transition moment directions in β-Ga2O3 from the polarization dependence of vibrational spectra,” Amanda Portoff, Andrew Venzie, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, J. Appl. Phys. 127, 055702 (2020).
  5.  “Trapping of multiple H atoms at the Ga(1) vacancy in β-Ga2O3,” W. Beall Fowler, Michael Stavola, Ying Qin, and Philip Weiser, Appl. Phys. Lett. 117, 142101 (2020).
  6.  “Vibrational properties of oxygen-hydrogen centers in H+ - and D+  -implanted Ga2O3,” Amanda Portoff, Andrew Venzie, Ying Qin, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, ECS J. Solid State Sci. Technol. 9, 125006 (2020).

  7. H. You, X. Lu, N. Task, Y. Yu, An asymptotically compatible approach for neumann-type boundary condition on nonlocal problems, ESAIM: Mathematical Modelling and Numerical Analysis 54 (4) (2020) 1373–1413. 

  8. C. H. Rycroft, C.-H. Wu, Y. Yu, K. Kamrin, An eulerian approach for modeling passive and active soft solids in fluids, Journal of Fluid Mechanics 898 (2020) A9. 

  9. M. D’Elia, X. Tian, Y. Yu, SIAM Journal on Scientific Computing 42 (4) (2020) A1935–A1949.

  10. M. D’Elia, X. Li, P. Seleson, X. Tian, Y. Yu, A review of local-to-nonlocal coupling methods in nonlocal diffusion and nonlocal mechanics, Journal of Peridynamics and Nonlocal Modeling (2020).

  11. H. You, Y. Yu, D. Kamensky, An asymptotically compatible formulation for local-to-nonlocal coupling problems without overlapping regions, Computer Methods in Applied Mechanics and Engineering 366 (2020) 113038. 

  12. D. Wei, T. Gao, Y. Yu, Dags with no fears: A closer look at continuous optimization for learning bayesian networks, Advances in Neural Information Processing Systems 33 (2020).

  13. L. Zhang, M. Yu, T. Gao, Y. Yu, Mcmh: Learning multi-chain multi-hop rules for knowledge graph rea soning, in: Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: Findings, 2020, pp. 3948–3954. 

  14. Y. Yu, T. Gao, Dags with no curl: Efficient dag structure learning, NeurIPS Workshop on Causal Discovery and Causality-Inspired Machine Learning (2020). 

  15. “Determination of dielectric axes and transition moment directions in β-Ga2O3 from the polarization dependence of vibrational spectra,” Amanda Portoff, Andrew Venzie, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, J. Appl. Phys. 127, 055702 (2020).
  16. “Trapping of multiple H atoms at the Ga(1) vacancy in β-Ga2O3,” W. Beall Fowler, Michael Stavola, Ying Qin, and Philip Weiser, Appl. Phys. Lett. 117, 142101 (2020).
  17. “Vibrational properties of oxygen-hydrogen centers in H+ - and D+  -implanted Ga2O3,” Amanda Portoff, Andrew Venzie, Ying Qin, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, ECS J. Solid State Sci. Technol. 9, 125006 (2020).
  18. Buskirk SW, Rokes AB, Lang GI. 2020. Adaptive evolution of nontransitive fitness in yeast. Elife. Dec 29;9:e62238. doi: 10.7554/eLife.62238.
  19. T.C. Chibueze and C.E. Ekuma and A.T. Raji and F.I. Ezema and C.M.I. Okoye, Tetragonal and uniaxial strains in pristine and doped half-Heusler AuMnSn alloy, ournal of Alloys and Compounds, 2020, 848, 156186 (DOI: 10.1016/j.jallcom.2020.156186)
  20. C.E. Ekuma, Z.-L. Liu, Mechanical properties and hardness of boron pnicogens BX (X = N, P, As), Materialia, 2020, 14, 100904 (DOI: 10.1016/j.mtla.2020.100904)
  21. Egbo, Kingsley O. and Ekuma, Chinedu E. and Liu, Chao Ping and Yu, Kin Man, Efficient p-type doping of sputter-deposited NiO thin films with Li, Ag, and Cu acceptors, Phys. Rev. Materials, 2020, 4, 104603 (DOI: 10.1103/PhysRevMaterials.4.104603)

  22. Kingsley O. Egbo, Chao Ping Liu, Chinedu E. Ekuma, and Kin Man Yu , "Vacancy defects induced changes in the electronic and optical properties of NiO studied by spectroscopic ellipsometry and first-principles calculations", Journal of Applied Physics 128, 135705 (2020) (DOI: 10.1063/5.0021650)

  23. T C Chibueze and C E Ekuma and A T Raji and D P Rai and C M I Okoye, Ferromagnetic half-metallicity in half-Heusler {AuMnSn}:Te Alloy, Materials Research Express, 7, 076519 (2020) (DOI: 10.1088/2053-1591/ab88ff)

  24. K. Aziz and C. E. Ekuma, "Electronic and vibrational spectroscopy of miscible MgO–ZnO ternary alloys", Journal of Applied Physics 127, 075706 (2020) (DOI: 10.1063/1.5141363)


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title2019
  1. Adeli Koudehi M., Rutkowski D., and Vavylonis D., Organization of Associating or Crosslinked Actin Filaments in Confinement, 2019, Cytoskeleton, 76:532-548 DOI: 10.1002/cm.21565
  2. Xu T., Langouras C., Adeli Koudehi M., Vos B. E., Wang N., Koenderink G. H., Huang X., and Vavylonis D., Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX, 2019, Scientific Reports, 9:1717  DOI: 10.1038/s41598-018-37182-6
  3. “Hydrogen in Ga2O3,” Michael Stavola, W. Beall Fowler, Ying Qin, Philip Weiser, and Stephen Pearton, in Gallium Oxide, ed. by Stephen Pearton, Fan Ren, and Michael Mastro (Elsevier, 2019), pp. 169-210.
  4. “Hydrogen Centers in β-Ga2O3: Infrared Spectroscopy and Density Functional Theory,” Ying Qin, Michael Stavola, W. Beall Fowler, Philip Weiser, and Stephen J. Pearton, ECS J. Solid State Sci. Technol. 8, Q3103 (2019).
  5. Fisher KJ, Kryazhimskiy S, Lang GI. 2019. Detecting genetic interactions using parallel evolution in experimental populations. Philos Trans R Soc Lond B Biol Sci. Jul 22;374(1777):20180237. doi: 10.1098/rstb.2018.0237. PMID: 31154981.


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title2018
  1. Horan B. G., Zerze G., Kim Y. C, Vavylonis D., and Mittal J., Computational modeling highlights the role of the disordered Formin Homology 1 domain in profilin-actin transfer, 2018, FEBS Lett. 592:1804-1816. DOI: 10.1002/1873-3468.13088
  2. “Diffusivity of the interstitial hydrogen shallow donor in In2O3,” Ying Qin, Philip Weiser, Karla Villalta, Michael Stavola, W. Beall Fowler, Ivan Biaggio, and Lynn Boatner, J. Appl. Phys. 123, 161506 (2018).
  3. “Tutorial: Novel properties of defects in semiconductors revealed by their vibrational spectra,” Michael Stavola and W. Beall Fowler, J. Appl. Phys. 123, 161561 (2018).
  4. “Structure and vibrational properties of the dominant O-H center in β-Ga2O3,” Philip Weiser, Michael Stavola, W. Beall Fowler, Ying Qin, and Stephen Pearton, Appl. Phys. Lett. 112, 232104 (2018).

  5. Fisher KJ, Buskirk SW, Vignogna RC, Marad DA, and Lang GI. 2018. Adaptive genome duplication affects patterns of molecular evolution in Saccharomyces cerevisiae. PLoS Genetics. May 25;14(5):e1007396. doi: 10.1371/journal.pgen.1007396. PMID: 29799840

  6. Marad DM, Buskirk SW, and Lang GI. 2018. Altered access to beneficial mutations slows adaptation and biases fixed mutations in diploids. Nature Ecology & Evolution. May;2(5):882-889. doi: 10.1038/s41559-018-0503-9. PMID: 29581586


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title2017
  1. Buskirk SW, Peace RE, and Lang GI. 2017. Hitchhiking and epistasis give rise to cohort dynamics in adapting populations. Proc Natl Acad Sci U S A. 2017 Jul 18. pii: 201702314. doi: 10.1073/pnas.1702314114. PMID: 28720700


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title2016
  1. “Point Defects,” W. B. Fowler, in Reference Module in Materials Science and Materials Engineering, ed. by Saleem Hashmi (Oxford: Elsevier, 2016), pp. 1-5.
  2. “The structures of interstitial hydrogen centers in VO2 in the dilute limit from their vibrational properties and theory,” Weikai Yin, Ying Qin, W. Beall Fowler, Michael Stavola and Lynn A. Boatner, J. Phys.: Condens. Matter 28, 395401 (2016).
  3. “Symmetry and diffusivity of the interstitial hydrogen shallow-donor center in In2O3,” Philip Weiser, Ying Qin, Weikai Yin, Michael Stavola, W. Beall Fowler, and Lynn A. Boatner, Appl. Phys. Lett. 109, 202105 (2016).


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title2010-2015
  1. “Detailed structure of the H-N-H center in GaAsyN1-y revealed by vibrational spectroscopy under uniaxial stress,” L. Wen, F. Bekisli, M. Stavola, W. B. Fowler, R. Trotta, A. Polimeni, M. Capizzi, S. Rubini, and F. Martinelli, Phys. Rev. B 81, 233201 (2010).
  2.  “Hydrogen impurities and shallow donors in SnO2 studied by infrared spectroscopy,” Figen Bekisli, Michael Stavola, W. Beall Fowler, Lynn Boatner, Erik Spahr, and Gunter Lüpke, Phys. Rev. B 84, 035213 (2011).
  3.  “Microscopic structure of a VH4 center trapped by C in Si,” Chao Peng, Haoxiang Zhang, Michael Stavola, W. Beall Fowler, Benjamin Esham, Stefan K. Estreicher, Andris Docaj, Lode Carnel, and Mike Seacrist, Phys. Rev. B 84, 195205 (2011).
  4. “Bond angles for O-H defects in SnO2 from polarization properties of their vibrational modes,” Figen Bekisli, W. Beall Fowler, Michael Stavola, Lynn A. Boatner, Erik Spahr, and Gunter Lüpke, Phys. Rev. B 85, 205202 (2012).
  5. “Microscopic origin of compressive strain in hydrogen-irradiated dilute GaAs1-yNy alloys: Role of  N-Hn centers with n>2 and their thermal stability,” L. Wen, M. Stavola, W. B. Fowler, S. Kleekajai, R. Trotta, A. Polimeni, M. Xapizzi, S. Rubini, F. Martelli, and C. W. Tu, Phys. Rev. B 86, 085206 (2012).
  6.  “Small polaron characteristics of an OD center in TiO2 studied by infrared spectroscopy,” Figen Bekisli, W. Beall Fowler, and Michael Stavola, Phys. Rev. B 86, 155208 (2012).
  7. “Contrasting the experimental properties of hydrogen in SnO2, In2O3, and TiO2,” Michael Stavola, Figen Bekisli, Weikai Yin, Kirby Smithe, W. Beall Fowler and Lynn A. Boatner, J. Appl. Phys. 115, 012001 (2014). 
  8. “Hydrogen centers and the conductivity of In2O3 single crystals,” Weikai Yin, Kirby Smithe, Philip Weiser, Michael Stavola, W. Beall Fowler, Lynn Boatner, Stephen J. Pearton, David C. Hays, and Sandro G. Koch, Phys. Rev. B 91, 075208 (2015).
  9. “Microscopic Structure of N-Hn Complexes in Dilute Nitride Semiconductors Revealed by Their Vibrational Properties,” Michael Stavola and W. Beall Fowler, in Hydrogenated Dilute Nitride Semiconductors, ed. by Gianluca Ciatto  (Pan Stanford, 2015), pp. 129-160.


Presentations

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title2021
  • Cytoskeletal and membrane flows for cell motility and polarization (D. Vavylonis), Talk at Mathematics of the Cell: Integrating Signaling, Transport and Mechanics, Banff International Research Station October 2021
  • Discrete mechanical model of lamellipodial actin networks (David Rutkowski, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Model of dendritic actin network with distributed turnover and structural remodeling (Danielle Holz, Aaron Hall, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Coarse-grained simulations of actin polymerization (Aaron Hall, Brandon Horan, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Turnover, Mechanics, And Structural Plasticity of Lamellipodial Actin Networks, Invited Speaker, “Building the Cell, 20 Years After” Subgroup, Cell Bio Virtual 2020 (D. Vavylonis, ASCB/EMBO Annual meeting) December 2020
  • Discrete mechanical model of lamellipodial actin networks (David Rutkowski, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Model of dendritic actin network with distributed turnover and structural remodeling (Danielle Holz, Aaron Hall, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Coarse-grained simulations of actin polymerization (Aaron Hall, Brandon Horan, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021

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